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1. A draft human pangenome reference

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K, Monlong, Jean, Abel, Haley J, Buonaiuto, Silvia, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M, Feng, Xiaowen, Fischer, Christian, Fulton, Robert S, Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T, Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J, Mitchell, Matthew W, Munson, Katherine M, Mwaniki, Moses Njagi, Novak, Adam M, Olsen, Hugh E, Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A, Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R, Antonacci-Fulton, Lucinda L, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Korbel, Jan O, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D, Popejoy, Alice B, Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A, Rhie, Arang, Sacco, Samuel, Sanders, Ashley D, Schneider, Valerie A, Schultz, Baergen I, Shafin, Kishwar, Smith, Michael W, Sofia, Heidi J, Abou Tayoun, Ahmad N, Thibaud-Nissen, Françoise, and Tricomi, Francesca Floriana

Subjects
Biological Sciences, Genetics, 2.1 Biological and endogenous factors, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Humans, Diploidy, Genome, Human, Haplotypes, Sequence Analysis, DNA, Genomics, Reference Standards, Cohort Studies, Alleles, Genetic Variation, General Science & Technology
Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Published
2023

2. Semi-automated assembly of high-quality diploid human reference genomes

Author

Jarvis, Erich D, Formenti, Giulio, Rhie, Arang, Guarracino, Andrea, Yang, Chentao, Wood, Jonathan, Tracey, Alan, Thibaud-Nissen, Francoise, Vollger, Mitchell R, Porubsky, David, Cheng, Haoyu, Asri, Mobin, Logsdon, Glennis A, Carnevali, Paolo, Chaisson, Mark JP, Chin, Chen-Shan, Cody, Sarah, Collins, Joanna, Ebert, Peter, Escalona, Merly, Fedrigo, Olivier, Fulton, Robert S, Fulton, Lucinda L, Garg, Shilpa, Gerton, Jennifer L, Ghurye, Jay, Granat, Anastasiya, Green, Richard E, Harvey, William, Hasenfeld, Patrick, Hastie, Alex, Haukness, Marina, Jaeger, Erich B, Jain, Miten, Kirsche, Melanie, Kolmogorov, Mikhail, Korbel, Jan O, Koren, Sergey, Korlach, Jonas, Lee, Joyce, Li, Daofeng, Lindsay, Tina, Lucas, Julian, Luo, Feng, Marschall, Tobias, Mitchell, Matthew W, McDaniel, Jennifer, Nie, Fan, Olsen, Hugh E, Olson, Nathan D, Pesout, Trevor, Potapova, Tamara, Puiu, Daniela, Regier, Allison, Ruan, Jue, Salzberg, Steven L, Sanders, Ashley D, Schatz, Michael C, Schmitt, Anthony, Schneider, Valerie A, Selvaraj, Siddarth, Shafin, Kishwar, Shumate, Alaina, Stitziel, Nathan O, Stober, Catherine, Torrance, James, Wagner, Justin, Wang, Jianxin, Wenger, Aaron, Xiao, Chuanle, Zimin, Aleksey V, Zhang, Guojie, Wang, Ting, Li, Heng, Garrison, Erik, Haussler, David, Hall, Ira, Zook, Justin M, Eichler, Evan E, Phillippy, Adam M, Paten, Benedict, Howe, Kerstin, and Miga, Karen H

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Humans, Chromosome Mapping, Diploidy, Genome, Human, Haplotypes, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Reference Standards, Genomics, Chromosomes, Human, Genetic Variation, Human Pangenome Reference Consortium, General Science & Technology
Abstract

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

Published
2022

3. Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences

Author

Ganel, Liron, Chen, Lei, Christ, Ryan, Vangipurapu, Jagadish, Young, Erica, Das, Indraniel, Kanchi, Krishna, Larson, David, Regier, Allison, Abel, Haley, Kang, Chul Joo, Scott, Alexandra, Havulinna, Aki, Chiang, Charleston WK, Service, Susan, Freimer, Nelson, Palotie, Aarno, Ripatti, Samuli, Kuusisto, Johanna, Boehnke, Michael, Laakso, Markku, Locke, Adam, Stitziel, Nathan O, and Hall, Ira M

Subjects
Biological Sciences, Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Adult, Aged, Apoptosis Regulatory Proteins, Cell Lineage, DNA Copy Number Variations, DNA, Mitochondrial, Female, GTP-Binding Proteins, Genetic Predisposition to Disease, Genome, Mitochondrial, Genome-Wide Association Study, Humans, Male, Membrane Proteins, Mendelian Randomization Analysis, Middle Aged, Phenotype, Polymorphism, Single Nucleotide, Proto-Oncogene Proteins c-myb, Sequence Analysis, DNA, Exome Sequencing, Metabolic syndrome, Mitochondrial content, Human genetics, Human genome sequencing, Genome-wide association studies, Mendelian randomization, Genetics & Heredity, Biochemistry and cell biology
Abstract

BackgroundMitochondrial genome copy number (MT-CN) varies among humans and across tissues and is highly heritable, but its causes and consequences are not well understood. When measured by bulk DNA sequencing in blood, MT-CN may reflect a combination of the number of mitochondria per cell and cell-type composition. Here, we studied MT-CN variation in blood-derived DNA from 19184 Finnish individuals using a combination of genome (N = 4163) and exome sequencing (N = 19034) data as well as imputed genotypes (N = 17718).ResultsWe identified two loci significantly associated with MT-CN variation: a common variant at the MYB-HBS1L locus (P = 1.6 × 10-8), which has previously been associated with numerous hematological parameters; and a burden of rare variants in the TMBIM1 gene (P = 3.0 × 10-8), which has been reported to protect against non-alcoholic fatty liver disease. We also found that MT-CN is strongly associated with insulin levels (P = 2.0 × 10-21) and other metabolic syndrome (metS)-related traits. Using a Mendelian randomization framework, we show evidence that MT-CN measured in blood is causally related to insulin levels. We then applied an MT-CN polygenic risk score (PRS) derived from Finnish data to the UK Biobank, where the association between the PRS and metS traits was replicated. Adjusting for cell counts largely eliminated these signals, suggesting that MT-CN affects metS via cell-type composition.ConclusionThese results suggest that measurements of MT-CN in blood-derived DNA partially reflect differences in cell-type composition and that these differences are causally linked to insulin and related traits.

Published
2021

4. Association of structural variation with cardiometabolic traits in Finns

Author

Chen, Lei, Abel, Haley J, Das, Indraniel, Larson, David E, Ganel, Liron, Kanchi, Krishna L, Regier, Allison A, Young, Erica P, Kang, Chul Joo, Scott, Alexandra J, Chiang, Colby, Wang, Xinxin, Lu, Shuangjia, Christ, Ryan, Service, Susan K, Chiang, Charleston WK, Havulinna, Aki S, Kuusisto, Johanna, Boehnke, Michael, Laakso, Markku, Palotie, Aarno, Ripatti, Samuli, Freimer, Nelson B, Locke, Adam E, Stitziel, Nathan O, and Hall, Ira M

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Alleles, Cardiovascular Diseases, Cholesterol, DNA Copy Number Variations, Female, Finland, Genome, Human, Genomic Structural Variation, Genotype, High-Throughput Nucleotide Sequencing, Humans, Male, Mitochondrial Proteins, Promoter Regions, Genetic, Pyruvate Dehydrogenase (Lipoamide)-Phosphatase, Pyruvic Acid, Serum Albumin, Human, Finnish population, cardiometabolic traits, genome-wide association study, structural variation, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10-54) and is also associated with increased levels of total cholesterol (p = 1.22 × 10-28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10-21) and alanine (p = 6.14 × 10-12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10-10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10-35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk.

Published
2021

5. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Lee, HoJoon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Olson, Nathan D., Puiu, Daniela, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sirén, Jouni, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M.D., Zimin, Aleksey V., Popejoy, Alice B., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Jarvis, Erich D., Miga, Karen H., Wang, Ting, Garrison, Erik, Marschall, Tobias, Hall, Ira, Li, Heng, Paten, Benedict, Greer, Stephanie U., Pavlichin, Dmitri S., Zhou, Bo, Urban, Alexander E., and Weissman, Tsachy

Published
2023
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6. Mapping and characterization of structural variation in 17,795 human genomes

Author

Abel, Haley J, Larson, David E, Regier, Allison A, Chiang, Colby, Das, Indraniel, Kanchi, Krishna L, Layer, Ryan M, Neale, Benjamin M, Salerno, William J, Reeves, Catherine, Buyske, Steven, Matise, Tara C, Muzny, Donna M, Zody, Michael C, Lander, Eric S, Dutcher, Susan K, Stitziel, Nathan O, and Hall, Ira M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Generic health relevance, Alleles, Case-Control Studies, Epigenesis, Genetic, Female, Gene Dosage, Genetic Variation, Genetics, Population, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Male, Molecular Sequence Annotation, Quantitative Trait Loci, Racial Groups, Software, Whole Genome Sequencing, NHGRI Centers for Common Disease Genomics, General Science & Technology
Abstract

A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and resources for the study of structural variants have lagged behind those for smaller variants. Here we used a scalable pipeline1 to map and characterize structural variants in 17,795 deeply sequenced human genomes. We publicly release site-frequency data to create the largest, to our knowledge, whole-genome-sequencing-based structural variant resource so far. On average, individuals carry 2.9 rare structural variants that alter coding regions; these variants affect the dosage or structure of 4.2 genes and account for 4.0-11.2% of rare high-impact coding alleles. Using a computational model, we estimate that structural variants account for 17.2% of rare alleles genome-wide, with predicted deleterious effects that are equivalent to loss-of-function coding alleles; approximately 90% of such structural variants are noncoding deletions (mean 19.1 per genome). We report 158,991 ultra-rare structural variants and show that 2% of individuals carry ultra-rare megabase-scale structural variants, nearly half of which are balanced or complex rearrangements. Finally, we infer the dosage sensitivity of genes and noncoding elements, and reveal trends that relate to element class and conservation. This work will help to guide the analysis and interpretation of structural variants in the era of whole-genome sequencing.

Published
2020

7. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

Author

Eichler, Evan E., Korbel, Jan O., Lee, Charles, Marschall, Tobias, Devine, Scott E., Harvey, William T., Zhou, Weichen, Mills, Ryan E., Rausch, Tobias, Kumar, Sushant, Alkan, Can, Hormozdiari, Fereydoun, Chong, Zechen, Chen, Yu, Yang, Xiaofei, Lin, Jiadong, Gerstein, Mark B., Kai, Ye, Zhu, Qihui, Yilmaz, Feyza, Xiao, Chunlin, Byrska-Bishop, Marta, Evani, Uday S., Zhao, Xuefang, Basile, Anna O., Abel, Haley J., Regier, Allison A., Corvelo, André, Clarke, Wayne E., Musunuri, Rajeeva, Nagulapalli, Kshithija, Fairley, Susan, Runnels, Alexi, Winterkorn, Lara, Lowy, Ernesto, Paul Flicek, Germer, Soren, Brand, Harrison, Hall, Ira M., Talkowski, Michael E., Narzisi, Giuseppe, and Zody, Michael C.

Published
2022
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8. Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants

Author

Gerstein, Mark B., Sanders, Ashley D., Zody, Micheal C., Talkowski, Michael E., Mills, Ryan E., Korbel, Jan O., Marschall, Tobias, Ebert, Peter, Audano, Peter A., Rodriguez-Martin, Bernardo, Porubsky, David, Jan Bonder, Marc, Sulovari, Arvis, Ebler, Jana, Zhou, Weichen, Serra Mari, Rebecca, Yilmaz, Feyza, Zhao, Xuefang, Hsieh, PingHsun, Lee, Joyce, Kumar, Sushant, Rausch, Tobias, Chen, Yu, Chong, Zechen, Munson, Katherine M., Chaisson, Mark J.P., Chen, Junjie, Shi, Xinghua, Wenger, Aaron M., Harvey, William T., Hansenfeld, Patrick, Regier, Allison, Hall, Ira M., Flicek, Paul, Hastie, Alex R., Fairely, Susan, Lin, Jiadong, Yang, Xiaofei, Kosters, Walter, Xu, Tun, Jia, Yanyan, Wang, Songbo, Zhu, Qihui, Ryan, Mallory, Guo, Li, Zhang, Chengsheng, Lee, Charles, Devine, Scott E., Eichler, Evan E., and Ye, Kai

Published
2022
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9. A strategy for building and using a human reference pangenome.

Author

Llamas, Bastien, Narzisi, Giuseppe, Schneider, Valerie, Audano, Peter, Biederstedt, Evan, Blauvelt, Lon, Bradbury, Peter, Chang, Xian, Chin, Chen-Shan, Fungtammasan, Arkarachai, Clarke, Wayne, Cleary, Alan, Ebler, Jana, Eizenga, Jordan, Sibbesen, Jonas, Markello, Charles, Garrison, Erik, Garg, Shilpa, Hickey, Glenn, Lazo, Gerard, Lin, Michael, Mahmoud, Medhat, Marschall, Tobias, Minkin, Ilia, Musunuri, Rajeeva, Sagayaradj, Sagayamary, Novak, Adam, Rautiainen, Mikko, Regier, Allison, Sedlazeck, Fritz, Siren, Jouni, Souilmi, Yassine, Wagner, Justin, Wrightsman, Travis, Yokoyama, Toshiyuki, Zeng, Qiandong, Zook, Justin, Paten, Benedict, Busby, Ben, and Monlong, Jean

Abstract

In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.

Published
2019

10. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author

Lee, HoJoon, primary, Greer, Stephanie U., additional, Pavlichin, Dmitri S., additional, Zhou, Bo, additional, Urban, Alexander E., additional, Weissman, Tsachy, additional, Ji, Hanlee P., additional, Liao, Wen-Wei, additional, Asri, Mobin, additional, Ebler, Jana, additional, Doerr, Daniel, additional, Haukness, Marina, additional, Hickey, Glenn, additional, Lu, Shuangjia, additional, Lucas, Julian K., additional, Monlong, Jean, additional, Abel, Haley J., additional, Buonaiuto, Silvia, additional, Chang, Xian H., additional, Cheng, Haoyu, additional, Chu, Justin, additional, Colonna, Vincenza, additional, Eizenga, Jordan M., additional, Feng, Xiaowen, additional, Fischer, Christian, additional, Fulton, Robert S., additional, Garg, Shilpa, additional, Groza, Cristian, additional, Guarracino, Andrea, additional, Harvey, William T., additional, Heumos, Simon, additional, Howe, Kerstin, additional, Jain, Miten, additional, Lu, Tsung-Yu, additional, Markello, Charles, additional, Martin, Fergal J., additional, Mitchell, Matthew W., additional, Munson, Katherine M., additional, Mwaniki, Moses Njagi, additional, Novak, Adam M., additional, Olsen, Hugh E., additional, Pesout, Trevor, additional, Porubsky, David, additional, Prins, Pjotr, additional, Sibbesen, Jonas A., additional, Tomlinson, Chad, additional, Villani, Flavia, additional, Vollger, Mitchell R., additional, Antonacci-Fulton, Lucinda L., additional, Baid, Gunjan, additional, Baker, Carl A., additional, Belyaeva, Anastasiya, additional, Billis, Konstantinos, additional, Carroll, Andrew, additional, Chang, Pi-Chuan, additional, Cody, Sarah, additional, Cook, Daniel E., additional, Cornejo, Omar E., additional, Diekhans, Mark, additional, Ebert, Peter, additional, Fairley, Susan, additional, Fedrigo, Olivier, additional, Felsenfeld, Adam L., additional, Formenti, Giulio, additional, Frankish, Adam, additional, Gao, Yan, additional, Giron, Carlos Garcia, additional, Green, Richard E., additional, Haggerty, Leanne, additional, Hoekzema, Kendra, additional, Hourlier, Thibaut, additional, Kolesnikov, Alexey, additional, Korbel, Jan O., additional, Kordosky, Jennifer, additional, Lee, HoJoon, additional, Lewis, Alexandra P., additional, Magalhães, Hugo, additional, Marco-Sola, Santiago, additional, Marijon, Pierre, additional, McDaniel, Jennifer, additional, Mountcastle, Jacquelyn, additional, Nattestad, Maria, additional, Olson, Nathan D., additional, Puiu, Daniela, additional, Regier, Allison A., additional, Rhie, Arang, additional, Sacco, Samuel, additional, Sanders, Ashley D., additional, Schneider, Valerie A., additional, Schultz, Baergen I., additional, Shafin, Kishwar, additional, Sirén, Jouni, additional, Smith, Michael W., additional, Sofia, Heidi J., additional, Abou Tayoun, Ahmad N., additional, Thibaud-Nissen, Françoise, additional, Tricomi, Francesca Floriana, additional, Wagner, Justin, additional, Wood, Jonathan M.D., additional, Zimin, Aleksey V., additional, Popejoy, Alice B., additional, Bourque, Guillaume, additional, Chaisson, Mark J.P., additional, Flicek, Paul, additional, Phillippy, Adam M., additional, Zook, Justin M., additional, Eichler, Evan E., additional, Haussler, David, additional, Jarvis, Erich D., additional, Miga, Karen H., additional, Wang, Ting, additional, Garrison, Erik, additional, Marschall, Tobias, additional, Hall, Ira, additional, Li, Heng, additional, and Paten, Benedict, additional

Published
2023
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11. A draft human pangenome reference

Author

Liao, Wen Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi Chuan, Cody, Sarah, Cook, Daniel E., Cook-Deegan, Robert M., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kenny, Eimear E., Koenig, Barbara A., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, Ho Joon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Walenz, Brian, Wood, Jonathan M.D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Jarvis, Erich D., Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, Paten, Benedict, Liao, Wen Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi Chuan, Cody, Sarah, Cook, Daniel E., Cook-Deegan, Robert M., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kenny, Eimear E., Koenig, Barbara A., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, Ho Joon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Walenz, Brian, Wood, Jonathan M.D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Jarvis, Erich D., Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, and Paten, Benedict

Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals 1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Published
2023

12. Alignment and Analysis of Closely Related Genomes

Author

Regier, Allison, Olson, Michael, Emrich, Scott J., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, and Rajasekaran, Sanguthevar, editor

Published
2009
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13. Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

Author

Regier, Allison A., Farjoun, Yossi, Larson, David E., Krasheninina, Olga, Kang, Hyun Min, Howrigan, Daniel P., Chen, Bo-Juen, Kher, Manisha, Banks, Eric, Ames, Darren C., English, Adam C., Li, Heng, Xing, Jinchuan, Zhang, Yeting, Matise, Tara, Abecasis, Goncalo R., Salerno, Will, Zody, Michael C., Neale, Benjamin M., and Hall, Ira M.

Published
2018
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14. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

Author

Kirkness, Ewen F., Haas, Brian J., Sun, Weilin, Braig, Henk R., Perotti, M. Alejandra, Clark, John M., Lee, Si Hyeock, Robertson, Hugh M., Kennedy, Ryan C., Elhaik, Eran, Gerlach, Daniel, Kriventseva, Evgenia V., Elsik, Christine G., Graur, Dan, Hill, Catherine A., Veenstra, Jan A., Walenz, Brian, Tubío, José Manuel C., Ribeiro, José M. C., Rozas, Julio, Johnston, J. Spencer, Reese, Justin T., Popadic, Aleksandar, Tojo, Marta, Raoult, Didier, Reed, David L., Tomoyasu, Yoshinori, Krause, Emily, Mittapalli, Omprakash, Margam, Venu M., Li, Hong-Mei, Meyer, Jason M., Johnson, Reed M., Romero-Severson, Jeanne, VanZee, Janice Pagel, Alvarez-Ponce, David, Vieira, Filipe G., Aguadé, Montserrat, Guirao-Rico, Sara, Anzola, Juan M., Yoon, Kyong S., Strycharz, Joseph P., Unger, Maria F., Christley, Scott, Lobo, Neil F., Seufferheld, Manfredo J., Wang, NaiKuan, Dasch, Gregory A., Struchiner, Claudio J., Madey, Greg, Hannick, Linda I., Bidwell, Shelby, Joardar, Vinita, Caler, Elisabet, Shao, Renfu, Barker, Stephen C., Cameron, Stephen, Bruggner, Robert V., Regier, Allison, Johnson, Justin, Viswanathan, Lakshmi, Utterback, Terry R., Sutton, Granger G., Lawson, Daniel, Waterhouse, Robert M., Venter, J. Craig, Strausberg, Robert L., Berenbaum, May R., Collins, Frank H., Zdobnov, Evgeny M., and Pittendrigh, Barry R.

Published
2010

15. Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants

Author

Lin, Jiadong, primary, Yang, Xiaofei, additional, Kosters, Walter, additional, Xu, Tun, additional, Jia, Yanyan, additional, Wang, Songbo, additional, Zhu, Qihui, additional, Ryan, Mallory, additional, Guo, Li, additional, Zhang, Chengsheng, additional, Lee, Charles, additional, Devine, Scott E., additional, Eichler, Evan E., additional, Ye, Kai, additional, Gerstein, Mark B., additional, Sanders, Ashley D., additional, Zody, Micheal C., additional, Talkowski, Michael E., additional, Mills, Ryan E., additional, Korbel, Jan O., additional, Marschall, Tobias, additional, Ebert, Peter, additional, Audano, Peter A., additional, Rodriguez-Martin, Bernardo, additional, Porubsky, David, additional, Jan Bonder, Marc, additional, Sulovari, Arvis, additional, Ebler, Jana, additional, Zhou, Weichen, additional, Serra Mari, Rebecca, additional, Yilmaz, Feyza, additional, Zhao, Xuefang, additional, Hsieh, PingHsun, additional, Lee, Joyce, additional, Kumar, Sushant, additional, Rausch, Tobias, additional, Chen, Yu, additional, Chong, Zechen, additional, Munson, Katherine M., additional, Chaisson, Mark J.P., additional, Chen, Junjie, additional, Shi, Xinghua, additional, Wenger, Aaron M., additional, Harvey, William T., additional, Hansenfeld, Patrick, additional, Regier, Allison, additional, Hall, Ira M., additional, Flicek, Paul, additional, Hastie, Alex R., additional, and Fairely, Susan, additional

Published
2022
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16. Additional file 3 of Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences

Author

Ganel, Liron, Chen, Lei, Christ, Ryan, Vangipurapu, Jagadish, Young, Erica, Das, Indraniel, Kanchi, Krishna, Larson, David, Regier, Allison, Abel, Haley, Kang, Chul Joo, Scott, Alexandra, Havulinna, Aki, Chiang, Charleston W. K., Service, Susan, Freimer, Nelson, Palotie, Aarno, Ripatti, Samuli, Kuusisto, Johanna, Boehnke, Michael, Laakso, Markku, Locke, Adam, Stitziel, Nathan O., and Hall, Ira M.

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING
Abstract

Additional file 3:. PDF format. Supplementary Methods. Describes methods in further detail than the main text.

Published
2021
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17. Additional file 6 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Abstract

Additional file 6:Distance between consecutive de novo SNPs. The distance between consecutive de novo SNPs were calculated to detect SNP clustering characteristic of sequencing errors or mis-mapping errors. 35% of the de novo SNPs were clustered in distances of less than 5 bps. (DOC 42 KB)

Published
2021
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18. Additional file 3 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Abstract

Additional file 3:Refined views of previously unknown COs shown in Figure3. Previously unknown COs detected in the progeny lines (highlighted with black bars in Figure 3) are indicated by double arrows in the chromosomal view (top) and zoomed-in view (boxed, bottom). (A-D) previously unknown COs in 7C126, (E-H) previously unknown COs in SC05. SNP map by 454 sequencing is presented in comparison with the MS marker linkage map in P. falciparum[4]. Each line represents a single SNP marker. HB3 alleles are shown in green bars and Dd2 alleles are shown in red. (PDF 183 KB)

Published
2021
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19. Additional file 8 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Subjects
mental disorders
Abstract

Additional file 8:Alternate SNP positions. The alternate SNP positions were assessed for their primary and secondary positions base call identity. Most primary base calls reflected the parental base call. The secondary base call position varied in the 2 progeny genomes in base call identity. Majority of the secondary base calls were parental in 7C126, whereas majority of the secondary base calls were non-parental in SC05 (A). Majority of the primary base calls were transitions in 7C126, while they were transversions in SC05 (B, C). (DOC 45 KB)

Published
2021
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20. Additional file 7 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Abstract

Additional file 7:Base conversion trends in de novo SNPs. The type of base conversion was investigated for positions at which the parental base calls were identical. More transversions were detected for SC05 compared to 7C126 (A), but did not show a predominant base conversion bias from 7C126 (B). (DOC 36 KB)

Published
2021
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21. Additional file 4 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Abstract

Additional file 4:Visual inspection of mapped WGS sequence at CO and NCO gene conversion breakpoints shown in Figure4. (A) simple CO breakpoint in 7C126, (B) NCO gene conversion in SC05 and (C) complex CO breakpoint accompanied by a conversion tract (defined by rapid allele changes at/near breakpoint) detected in 7C126. Chromosomal alignments at CO and NCO regions were visually inspected in comparison with the parental genomes, using Integrative Genomics Viewer [45]. (i) SNPs detected by 454 sequencing are ordered according to the chromosomal location (PlasmoDB v5.4 [27]). Each line represents a single SNP marker. HB3 alleles are shown in green bars and Dd2 alleles are shown in red. (ii) Comparison of SNPS and read alignments at selected SNP loci (arrow). SNPs are highlighted in blue [C], red [T], green [A] and brown [G]. (PDF 486 KB)

Published
2021
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22. Additional file 1 of Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences

Author

Ganel, Liron, Chen, Lei, Christ, Ryan, Vangipurapu, Jagadish, Young, Erica, Das, Indraniel, Kanchi, Krishna, Larson, David, Regier, Allison, Abel, Haley, Kang, Chul Joo, Scott, Alexandra, Havulinna, Aki, Chiang, Charleston W. K., Service, Susan, Freimer, Nelson, Palotie, Aarno, Ripatti, Samuli, Kuusisto, Johanna, Boehnke, Michael, Laakso, Markku, Locke, Adam, Stitziel, Nathan O., and Hall, Ira M.

Abstract

Additional file 1:. PDF format. Supplementary Figures and Small Supplementary Tables. Contains Figures S1-S8 and Tables S2-S4, S9, and S11.

Published
2021
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23. A strategy for building and using a human reference pangenome

Author

Llamas, Bastien, primary, Narzisi, Giuseppe, additional, Schneider, Valerie, additional, Audano, Peter A., additional, Biederstedt, Evan, additional, Blauvelt, Lon, additional, Bradbury, Peter, additional, Chang, Xian, additional, Chin, Chen-Shan, additional, Fungtammasan, Arkarachai, additional, Clarke, Wayne E., additional, Cleary, Alan, additional, Ebler, Jana, additional, Eizenga, Jordan, additional, Sibbesen, Jonas A., additional, Markello, Charles J., additional, Garrison, Erik, additional, Garg, Shilpa, additional, Hickey, Glenn, additional, Lazo, Gerard R., additional, Lin, Michael F., additional, Mahmoud, Medhat, additional, Marschall, Tobias, additional, Minkin, Ilia, additional, Monlong, Jean, additional, Musunuri, Rajeeva L., additional, Sagayaradj, Sagayamary, additional, Novak, Adam M., additional, Rautiainen, Mikko, additional, Regier, Allison, additional, Sedlazeck, Fritz J., additional, Siren, Jouni, additional, Souilmi, Yassine, additional, Wagner, Justin, additional, Wrightsman, Travis, additional, Yokoyama, Toshiyuki T., additional, Zeng, Qiandong, additional, Zook, Justin M., additional, Paten, Benedict, additional, and Busby, Ben, additional

Published
2021
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24. Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Author

Ebert, Peter, primary, Audano, Peter A., additional, Zhu, Qihui, additional, Rodriguez-Martin, Bernardo, additional, Porubsky, David, additional, Bonder, Marc Jan, additional, Sulovari, Arvis, additional, Ebler, Jana, additional, Zhou, Weichen, additional, Serra Mari, Rebecca, additional, Yilmaz, Feyza, additional, Zhao, Xuefang, additional, Hsieh, PingHsun, additional, Lee, Joyce, additional, Kumar, Sushant, additional, Lin, Jiadong, additional, Rausch, Tobias, additional, Chen, Yu, additional, Ren, Jingwen, additional, Santamarina, Martin, additional, Höps, Wolfram, additional, Ashraf, Hufsah, additional, Chuang, Nelson T., additional, Yang, Xiaofei, additional, Munson, Katherine M., additional, Lewis, Alexandra P., additional, Fairley, Susan, additional, Tallon, Luke J., additional, Clarke, Wayne E., additional, Basile, Anna O., additional, Byrska-Bishop, Marta, additional, Corvelo, André, additional, Evani, Uday S., additional, Lu, Tsung-Yu, additional, Chaisson, Mark J. P., additional, Chen, Junjie, additional, Li, Chong, additional, Brand, Harrison, additional, Wenger, Aaron M., additional, Ghareghani, Maryam, additional, Harvey, William T., additional, Raeder, Benjamin, additional, Hasenfeld, Patrick, additional, Regier, Allison A., additional, Abel, Haley J., additional, Hall, Ira M., additional, Flicek, Paul, additional, Stegle, Oliver, additional, Gerstein, Mark B., additional, Tubio, Jose M. C., additional, Mu, Zepeng, additional, Li, Yang I., additional, Shi, Xinghua, additional, Hastie, Alex R., additional, Ye, Kai, additional, Chong, Zechen, additional, Sanders, Ashley D., additional, Zody, Michael C., additional, Talkowski, Michael E., additional, Mills, Ryan E., additional, Devine, Scott E., additional, Lee, Charles, additional, Korbel, Jan O., additional, Marschall, Tobias, additional, and Eichler, Evan E., additional

Published
2021
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26. High Coverage Whole Genome Sequencing of the Expanded 1000 Genomes Project Cohort Including 602 Trios

Author

Byrska-Bishop, Marta, primary, Evani, Uday S., additional, Zhao, Xuefang, additional, Basile, Anna O., additional, Abel, Haley J., additional, Regier, Allison A., additional, Corvelo, André, additional, Clarke, Wayne E., additional, Musunuri, Rajeeva, additional, Nagulapalli, Kshithija, additional, Fairley, Susan, additional, Runnels, Alexi, additional, Winterkorn, Lara, additional, Lowy, Ernesto, additional, Consortium, The Human Genome Structural Variati, additional, Flicek, Paul, additional, Germer, Soren, additional, Brand, Harrison, additional, Hall, Ira M., additional, Talkowski, Michael E., additional, Narzisi, Giuseppe, additional, and Zody, Michael C., additional

Published
2021
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27. De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

Author

Ebert, Peter, primary, Audano, Peter A., additional, Zhu, Qihui, additional, Rodriguez-Martin, Bernardo, additional, Porubsky, David, additional, Bonder, Marc Jan, additional, Sulovari, Arvis, additional, Ebler, Jana, additional, Zhou, Weichen, additional, Mari, Rebecca Serra, additional, Yilmaz, Feyza, additional, Zhao, Xuefang, additional, Hsieh, PingHsun, additional, Lee, Joyce, additional, Kumar, Sushant, additional, Lin, Jiadong, additional, Rausch, Tobias, additional, Chen, Yu, additional, Ren, Jingwen, additional, Santamarina, Martin, additional, Höps, Wolfram, additional, Ashraf, Hufsah, additional, Chuang, Nelson T., additional, Yang, Xiaofei, additional, Munson, Katherine M., additional, Lewis, Alexandra P., additional, Fairley, Susan, additional, Tallon, Luke J., additional, Clarke, Wayne E., additional, Basile, Anna O., additional, Byrska-Bishop, Marta, additional, Corvelo, André, additional, Chaisson, Mark J.P., additional, Chen, Junjie, additional, Li, Chong, additional, Brand, Harrison, additional, Wenger, Aaron M., additional, Ghareghani, Maryam, additional, Harvey, William T., additional, Raeder, Benjamin, additional, Hasenfeld, Patrick, additional, Regier, Allison, additional, Abel, Haley, additional, Hall, Ira, additional, Flicek, Paul, additional, Stegle, Oliver, additional, Gerstein, Mark B., additional, Tubio, Jose M.C., additional, Mu, Zepeng, additional, Li, Yang I., additional, Shi, Xinghua, additional, Hastie, Alex R., additional, Ye, Kai, additional, Chong, Zechen, additional, Sanders, Ashley D., additional, Zody, Michael C., additional, Talkowski, Michael E., additional, Mills, Ryan E., additional, Devine, Scott E., additional, Lee, Charles, additional, Korbel, Jan O., additional, Marschall, Tobias, additional, and Eichler, Evan E., additional

Published
2020
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28. Association of Structural Variation with Cardiometabolic Traits in Finns

Author

Chen, Lei, primary, Abel, Haley J., additional, Das, Indraniel, additional, Larson, David E., additional, Ganel, Liron, additional, Kanchi, Krishna L., additional, Regier, Allison A., additional, Young, Erica P., additional, Kang, Chul Joo, additional, Scott, Alexandra J, additional, Chiang, Colby, additional, Wang, Xinxin, additional, Lu, Shuangjia, additional, Christ, Ryan, additional, Service, Susan K., additional, Chiang, Charleston W.K., additional, Havulinna, Aki S., additional, Kuusisto, Johanna, additional, Boehnke, Michael, additional, Laakso, Markku, additional, Palotie, Aarno, additional, Ripatti, Samuli, additional, Freimer, Nelson B., additional, Locke, Adam E., additional, Stitziel, Nathan O., additional, and Hall, Ira M., additional

Published
2020
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29. Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences

Author

Ganel, Liron, primary, Chen, Lei, additional, Christ, Ryan, additional, Vangipurapu, Jagadish, additional, Young, Erica, additional, Das, Indraniel, additional, Kanchi, Krishna, additional, Larson, David, additional, Regier, Allison, additional, Abel, Haley, additional, Kang, Chul Joo, additional, Scott, Alexandra, additional, Havulinna, Aki, additional, Chiang, Charleston W. K., additional, Service, Susan, additional, Freimer, Nelson, additional, Palotie, Aarno, additional, Ripatti, Samuli, additional, Kuusisto, Johanna, additional, Boehnke, Michael, additional, Laakso, Markku, additional, Locke, Adam, additional, Stitziel, Nathan O., additional, and Hall, Ira M., additional

Published
2020
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31. A strategy for building and using a human reference pangenome

Author

Llamas, Bastien, primary, Narzisi, Giuseppe, additional, Schneider, Valerie, additional, Audano, Peter A., additional, Biederstedt, Evan, additional, Blauvelt, Lon, additional, Bradbury, Peter, additional, Chang, Xian, additional, Chin, Chen-Shan, additional, Fungtammasan, Arkarachai, additional, Clarke, Wayne E., additional, Cleary, Alan, additional, Ebler, Jana, additional, Eizenga, Jordan, additional, Sibbesen, Jonas A., additional, Markello, Charles J., additional, Garrison, Erik, additional, Garg, Shilpa, additional, Hickey, Glenn, additional, Lazo, Gerard R., additional, Lin, Michael F., additional, Mahmoud, Medhat, additional, Marschall, Tobias, additional, Minkin, Ilia, additional, Monlong, Jean, additional, Musunuri, Rajeeva L., additional, Sagayaradj, Sagayamary, additional, Novak, Adam M., additional, Rautiainen, Mikko, additional, Regier, Allison, additional, Sedlazeck, Fritz J., additional, Siren, Jouni, additional, Souilmi, Yassine, additional, Wagner, Justin, additional, Wrightsman, Travis, additional, Yokoyama, Toshiyuki T., additional, Zeng, Qiandong, additional, Zook, Justin M., additional, Paten, Benedict, additional, and Busby, Ben, additional

Published
2019
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32. High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Tan John C, Collins Brendan, Desany Brian A, Tan Asako, Regier Allison, Samarakoon Upeka, Emrich Scott J, and Ferdig Michael T

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Knowledge of the origins, distribution, and inheritance of variation in the malaria parasite (Plasmodium falciparum) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenges to high-throughput sequencing technologies. We explore the viability of the Roche 454 Genome Sequencer FLX (GS FLX) high throughput sequencing technology for both whole genome sequencing and fine-resolution characterization of genetic exchange in malaria parasites. Results We present a scheme to survey recombination in the haploid stage genomes of two sibling parasite clones, using whole genome pyrosequencing that includes a sliding window approach to predict recombination breakpoints. Whole genome shotgun (WGS) sequencing generated approximately 2 million reads, with an average read length of approximately 300 bp. De novo assembly using a combination of WGS and 3 kb paired end libraries resulted in contigs ≤ 34 kb. More than 8,000 of the 24,599 SNP markers identified between parents were genotyped in the progeny, resulting in a marker density of approximately 1 marker/3.3 kb and allowing for the detection of previously unrecognized crossovers (COs) and many non crossover (NCO) gene conversions throughout the genome. Conclusions By sequencing the 23 Mb genomes of two haploid progeny clones derived from a genetic cross at more than 30× coverage, we captured high resolution information on COs, NCOs and genetic variation within the progeny genomes. This study is the first to resequence progeny clones to examine fine structure of COs and NCOs in malaria parasites.

Published
2011
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33. Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

Author

Costantini Carlo, Traore Sekou F, Emrich Scott J, Sharakhova Maria V, Bretz David A, Reidenbach Kyanne R, Regier Allison A, Sangaré Djibril M, Lobo Neil F, Besansky Nora J, and Collins Frank H

Subjects
Arctic medicine. Tropical medicine, RC955-962, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Alternative arrangements of chromosome 2 inversions in Anopheles gambiae are important sources of population structure, and are associated with adaptation to environmental heterogeneity. The forces responsible for their origin and maintenance are incompletely understood. Molecular characterization of inversion breakpoints provides insight into how they arose, and provides the basis for development of molecular karyotyping methods useful in future studies. Methods Sequence comparison of regions near the cytological breakpoints of 2Rb allowed the molecular delineation of breakpoint boundaries. Comparisons were made between the standard 2R+b arrangement in the An. gambiae PEST reference genome and the inverted 2Rb arrangements in the An. gambiae M and S genome assemblies. Sequence differences between alternative 2Rb arrangements were exploited in the design of a PCR diagnostic assay, which was evaluated against the known chromosomal banding pattern of laboratory colonies and field-collected samples from Mali and Cameroon. Results The breakpoints of the 7.55 Mb 2Rb inversion are flanked by extensive runs of the same short (72 bp) tandemly organized sequence, which was likely responsible for chromosomal breakage and rearrangement. Application of the molecular diagnostic assay suggested that 2Rb has a single common origin in An. gambiae and its sibling species, Anopheles arabiensis, and also that the standard arrangement (2R+b) may have arisen twice through breakpoint reuse. The molecular diagnostic was reliable when applied to laboratory colonies, but its accuracy was lower in natural populations. Conclusions The complex repetitive sequence flanking the 2Rb breakpoint region may be prone to structural and sequence-level instability. The 2Rb molecular diagnostic has immediate application in studies based on laboratory colonies, but its usefulness in natural populations awaits development of complementary molecular tools.

Published
2010
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34. Genome Modeling System: A Knowledge Management Platform for Genomics

Author

Griffith, Malachi, primary, Griffith, Obi L., additional, Smith, Scott M., additional, Ramu, Avinash, additional, Callaway, Matthew B., additional, Brummett, Anthony M., additional, Kiwala, Michael J., additional, Coffman, Adam C., additional, Regier, Allison A., additional, Oberkfell, Ben J., additional, Sanderson, Gabriel E., additional, Mooney, Thomas P., additional, Nutter, Nathaniel G., additional, Belter, Edward A., additional, Du, Feiyu, additional, Long, Robert L., additional, Abbott, Travis E., additional, Ferguson, Ian T., additional, Morton, David L., additional, Burnett, Mark M., additional, Weible, James V., additional, Peck, Joshua B., additional, Dukes, Adam, additional, McMichael, Joshua F., additional, Lolofie, Justin T., additional, Derickson, Brian R., additional, Hundal, Jasreet, additional, Skidmore, Zachary L., additional, Ainscough, Benjamin J., additional, Dees, Nathan D., additional, Schierding, William S., additional, Kandoth, Cyriac, additional, Kim, Kyung H., additional, Lu, Charles, additional, Harris, Christopher C., additional, Maher, Nicole, additional, Maher, Christopher A., additional, Magrini, Vincent J., additional, Abbott, Benjamin S., additional, Chen, Ken, additional, Clark, Eric, additional, Das, Indraniel, additional, Fan, Xian, additional, Hawkins, Amy E., additional, Hepler, Todd G., additional, Wylie, Todd N., additional, Leonard, Shawn M., additional, Schroeder, William E., additional, Shi, Xiaoqi, additional, Carmichael, Lynn K., additional, Weil, Matthew R., additional, Wohlstadter, Richard W., additional, Stiehr, Gary, additional, McLellan, Michael D., additional, Pohl, Craig S., additional, Miller, Christopher A., additional, Koboldt, Daniel C., additional, Walker, Jason R., additional, Eldred, James M., additional, Larson, David E., additional, Dooling, David J., additional, Ding, Li, additional, Mardis, Elaine R., additional, and Wilson, Richard K., additional

Published
2015
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36. Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

Author

Lobo, Neil F., Sangaré, Djibril M., Regier, Allison A., Reidenbach, Kyanne R., Bretz, David A., Sharakhova, Maria V., Emrich, Scott J., Traore, Sekou F., Costantini, Carlo, Besansky, Nora J., Collins, Frank H., Lobo, Neil F., Sangaré, Djibril M., Regier, Allison A., Reidenbach, Kyanne R., Bretz, David A., Sharakhova, Maria V., Emrich, Scott J., Traore, Sekou F., Costantini, Carlo, Besansky, Nora J., and Collins, Frank H.

Abstract

Background Alternative arrangements of chromosome 2 inversions in Anopheles gambiae are important sources of population structure, and are associated with adaptation to environmental heterogeneity. The forces responsible for their origin and maintenance are incompletely understood. Molecular characterization of inversion breakpoints provides insight into how they arose, and provides the basis for development of molecular karyotyping methods useful in future studies. Methods Sequence comparison of regions near the cytological breakpoints of 2Rb allowed the molecular delineation of breakpoint boundaries. Comparisons were made between the standard 2R+b arrangement in the An. gambiae PEST reference genome and the inverted 2Rb arrangements in the An. gambiae M and S genome assemblies. Sequence differences between alternative 2Rb arrangements were exploited in the design of a PCR diagnostic assay, which was evaluated against the known chromosomal banding pattern of laboratory colonies and field-collected samples from Mali and Cameroon. Results The breakpoints of the 7.55 Mb 2Rb inversion are flanked by extensive runs of the same short (72 bp) tandemly organized sequence, which was likely responsible for chromosomal breakage and rearrangement. Application of the molecular diagnostic assay suggested that 2Rb has a single common origin in An. gambiae and its sibling species, Anopheles arabiensis, and also that the standard arrangement (2R+b) may have arisen twice through breakpoint reuse. The molecular diagnostic was reliable when applied to laboratory colonies, but its accuracy was lower in natural populations. Conclusions The complex repetitive sequence flanking the 2Rb breakpoint region may be prone to structural and sequence-level instability. The 2Rb molecular diagnostic has immediate application in studies based on laboratory colonies, but its usefulness in natural populations awaits development of complementary molecular tools.

Published
2010
Full Text
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37. Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

Author

Entomology, Lobo, Neil F., Sangaré, Djibril M., Regier, Allison A., Reidenbach, Kyanne R., Bretz, David A., Sharakhova, Maria V., Emrich, Scott J., Traore, Sekou F., Costantini, Carlo, Besansky, Nora J., Collins, Frank H., Entomology, Lobo, Neil F., Sangaré, Djibril M., Regier, Allison A., Reidenbach, Kyanne R., Bretz, David A., Sharakhova, Maria V., Emrich, Scott J., Traore, Sekou F., Costantini, Carlo, Besansky, Nora J., and Collins, Frank H.

Abstract

Background Alternative arrangements of chromosome 2 inversions in Anopheles gambiae are important sources of population structure, and are associated with adaptation to environmental heterogeneity. The forces responsible for their origin and maintenance are incompletely understood. Molecular characterization of inversion breakpoints provides insight into how they arose, and provides the basis for development of molecular karyotyping methods useful in future studies. Methods Sequence comparison of regions near the cytological breakpoints of 2Rb allowed the molecular delineation of breakpoint boundaries. Comparisons were made between the standard 2R+b arrangement in the An. gambiae PEST reference genome and the inverted 2Rb arrangements in the An. gambiae M and S genome assemblies. Sequence differences between alternative 2Rb arrangements were exploited in the design of a PCR diagnostic assay, which was evaluated against the known chromosomal banding pattern of laboratory colonies and field-collected samples from Mali and Cameroon. Results The breakpoints of the 7.55 Mb 2Rb inversion are flanked by extensive runs of the same short (72 bp) tandemly organized sequence, which was likely responsible for chromosomal breakage and rearrangement. Application of the molecular diagnostic assay suggested that 2Rb has a single common origin in An. gambiae and its sibling species, Anopheles arabiensis, and also that the standard arrangement (2R+b) may have arisen twice through breakpoint reuse. The molecular diagnostic was reliable when applied to laboratory colonies, but its accuracy was lower in natural populations. Conclusions The complex repetitive sequence flanking the 2Rb breakpoint region may be prone to structural and sequence-level instability. The 2Rb molecular diagnostic has immediate application in studies based on laboratory colonies, but its usefulness in natural populations awaits development of complementary molecular tools.

Published
2010

38. Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

Author

Lobo, Neil F, primary, Sangaré, Djibril M, additional, Regier, Allison A, additional, Reidenbach, Kyanne R, additional, Bretz, David A, additional, Sharakhova, Maria V, additional, Emrich, Scott J, additional, Traore, Sekou F, additional, Costantini, Carlo, additional, Besansky, Nora J, additional, and Collins, Frank H, additional

Published
2010
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39. Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants

Author

Lin, Jiadong, Yang, Xiaofei, Kosters, Walter, Xu, Tun, Jia, Yanyan, Wang, Songbo, Zhu, Qihui, Ryan, Mallory, Guo, Li, Zhang, Chengsheng, Gerstein, Mark B., Sanders, Ashley D., Zody, Micheal C., Talkowski, Michael E., Mills, Ryan E., Korbel, Jan O., Marschall, Tobias, Ebert, Peter, Audano, Peter A., Rodriguez-Martin, Bernardo, Porubsky, David, Jan Bonder, Marc, Sulovari, Arvis, Ebler, Jana, Zhou, Weichen, Serra Mari, Rebecca, Yilmaz, Feyza, Zhao, Xuefang, Hsieh, PingHsun, Lee, Joyce, Kumar, Sushant, Rausch, Tobias, Chen, Yu, Chong, Zechen, Munson, Katherine M., Chaisson, Mark J.P., Chen, Junjie, Shi, Xinghua, Wenger, Aaron M., Harvey, William T., Hansenfeld, Patrick, Regier, Allison, Hall, Ira M., Flicek, Paul, Hastie, Alex R., Fairely, Susan, Lee, Charles, Devine, Scott E., Eichler, Evan E., and Ye, Kai

Abstract

Complex structural variants(CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants. However, detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match strategy. As a result, there has been limited progress for CSV discovery compared with simple structural variants. We systematically analyzed the multi-breakpoint connection feature of CSVs, and proposed Mako, utilizing a bottom-up guided model-free strategy, to detect CSVs from paired-end short-read sequencing. Specifically, we implemented a graph-based pattern growthapproach, where the graph depicts potential breakpoint connections, and pattern growth enables CSV detection without pre-defined models. Comprehensive evaluations on both simulated and real datasets revealed that Mako outperformed other algorithms. Notably, validation rates of CSV on real data based on experimental and computational validations as well as manual inspections are around 70%, where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp, respectively. Moreover, the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types, including two novel types of adjacent segments swap and tandem dispersed duplication. Further analysis of these CSVs also revealed the impact of sequence homology in the formation of CSVs. Mako is publicly available at https://github.com/xjtu-omics/Mako.

Published
2021
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49. Additional file 9 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Subjects
3. Good health
Abstract

Additional file 9:Selected CNVs in 7C126 and SC05. Comparative genomic hybridization (CGH) was used to detect large (> 1 kb) CNV regions in 7C126 (A) and SC05 (B). Five known CNVs that exist between parental strains were detected in the progeny in Chr 2, 5, 9 and 12. (PDF 129 KB)

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